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Merge pull request #168 from mlin865/stomachLayers
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Stomach layers
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@rchristie
rchristie authored Nov 13, 2021
2 parents a23f243 + 2f31737 commit f5eacc0
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5 changes: 3 additions & 2 deletions src/scaffoldmaker/annotation/bladder_terms.py
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("urethra junction of ventral bladder neck", "ILX:0738410")
]

def get_bladder_term(name : str):

def get_bladder_term(name: str):
"""
Find term by matching name to any identifier held for a term.
Raise exception if name not found.
:return ( preferred name, preferred id )
"""
for term in bladder_terms:
if name in term:
return ( term[0], term[1] )
return (term[0], term[1])
raise NameError("Bladder annotation term '" + name + "' not found.")
45 changes: 23 additions & 22 deletions src/scaffoldmaker/annotation/colon_terms.py
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# convention: preferred name, preferred id, followed by any other ids and alternative names
colon_terms = [
( "ascending colon", "UBERON:0001156", "FMA:14545", "ILX:0734393"),
( "descending colon", "UBERON:0001158", "FMA:14547", "ILX:0724444"),
( "caecum", "UBERON:0001153", "FMA:14541", "ILX:0732270"),
( "circular muscle layer of colon", "ILX:0772428"),
( "colon", "UBERON:0001155", "FMA:14543", "ILX:0736005"),
( "colonic mucosa", "UBERON:0000317", "FMA:14984", "ILX:0731046"),
( "distal colon", "UBERON:0008971", "ILX:0727523"),
( "longitudinal muscle layer of colon", "ILX:0775554"),
( "luminal surface of the colonic mucosa", "ILX:0793083"),
( "mesenteric zone", "None"),
( "non-mesenteric zone", "None"),
( "proximal colon", "UBERON:0008972", "ILX:0733240"),
( "serosa of colon", "UBERON:0003335", "FMA:14990", "ILX:0736932"),
( "spiral colon", "UBERON:0010239", "ILX:0735018"),
( "submucosa of colon", "UBERON:0003331", "FMA:14985", "ILX:0728041"),
( "taenia coli", "UBERON:0012419", "FMA:15041", "ILX:0731555"),
( "taenia libera", "ILX:0739285"),
( "taenia mesocolica", "ILX:0739284"),
( "taenia omentalis", "ILX:0739286"),
( "transverse colon", "UBERON:0001157", "FMA:14546", "ILX:0728767")
("ascending colon", "UBERON:0001156", "FMA:14545", "ILX:0734393"),
("descending colon", "UBERON:0001158", "FMA:14547", "ILX:0724444"),
("caecum", "UBERON:0001153", "FMA:14541", "ILX:0732270"),
("circular muscle layer of colon", "ILX:0772428"),
("colon", "UBERON:0001155", "FMA:14543", "ILX:0736005"),
("colonic mucosa", "UBERON:0000317", "FMA:14984", "ILX:0731046"),
("distal colon", "UBERON:0008971", "ILX:0727523"),
("longitudinal muscle layer of colon", "ILX:0775554"),
("luminal surface of the colonic mucosa", "ILX:0793083"),
("mesenteric zone", "None"),
("non-mesenteric zone", "None"),
("proximal colon", "UBERON:0008972", "ILX:0733240"),
("serosa of colon", "UBERON:0003335", "FMA:14990", "ILX:0736932"),
("spiral colon", "UBERON:0010239", "ILX:0735018"),
("submucosa of colon", "UBERON:0003331", "FMA:14985", "ILX:0728041"),
("taenia coli", "UBERON:0012419", "FMA:15041", "ILX:0731555"),
("taenia libera", "ILX:0739285"),
("taenia mesocolica", "ILX:0739284"),
("taenia omentalis", "ILX:0739286"),
("transverse colon", "UBERON:0001157", "FMA:14546", "ILX:0728767")
]

def get_colon_term(name : str):

def get_colon_term(name: str):
"""
Find term by matching name to any identifier held for a term.
Raise exception if name not found.
:return ( preferred name, preferred id )
"""
for term in colon_terms:
if name in term:
return ( term[0], term[1] )
return (term[0], term[1])
raise NameError("Colon annotation term '" + name + "' not found.")
13 changes: 7 additions & 6 deletions src/scaffoldmaker/annotation/smallintestine_terms.py
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# convention: preferred name, preferred id, followed by any other ids and alternative names
smallintestine_terms = [
( "duodenum", "UBERON:0002114", "FMA:7206", "ILX:0726125"),
( "ileum", "UBERON:0002116", "FMA:7208", "ILX:0728151"),
( "jejunum", "UBERON:0002115", "FMA:7207", "ILX:0724224"),
( "small intestine", "UBERON:0002108", "FMA:7200", "ILX:0726770")
("duodenum", "UBERON:0002114", "FMA:7206", "ILX:0726125"),
("ileum", "UBERON:0002116", "FMA:7208", "ILX:0728151"),
("jejunum", "UBERON:0002115", "FMA:7207", "ILX:0724224"),
("small intestine", "UBERON:0002108", "FMA:7200", "ILX:0726770")
]

def get_smallintestine_term(name : str):

def get_smallintestine_term(name: str):
"""
Find term by matching name to any identifier held for a term.
Raise exception if name not found.
:return ( preferred name, preferred id )
"""
for term in smallintestine_terms:
if name in term:
return ( term[0], term[1] )
return (term[0], term[1])
raise NameError("Small intestine annotation term '" + name + "' not found.")
107 changes: 74 additions & 33 deletions src/scaffoldmaker/annotation/stomach_terms.py
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# convention: preferred name, preferred id, followed by any other ids and alternative names
stomach_terms = [
( "antrum on serosa split margin", "None"),
( "body of stomach", "UBERON:0001161", " FMA:14560", "ILX:0724929"),
( "body on serosa split margin", "None"),
( "cardia of stomach", "UBERON:0001162", " FMA:14561", "ILX:0729096"),
( "dorsal stomach", "None"),
( "duodenum", "UBERON:0002114", " FMA:7206", "ILX:0726125"),
( "duodenum on greater curvature", "None"),
( "esophagus", "UBERON:0001043", "FMA: 7131", "ILX:0735017"),
( "esophagus on serosa split margin", "None"),
( "esophagogastric junction", "UBERON:0007650", "FMA: 9434", "ILX:0733910"),
( "forestomach-glandular stomach junction", "UBERON:0012270", "ILX:0729974"),
( "forestomach-glandular stomach junction on inner wall", "None"),
( "forestomach-glandular stomach junction on outer wall", "None"),
( "fundus of stomach", "UBERON:0001160", " FMA:14559", "ILX:0724443"),
( "fundus on serosa split margin", "None"),
( "gastro-esophagal junction on lesser curvature", "None"),
#( "greater curvature of stomach", "UBERON:0001164", "FMA: 14574", "ILX:0724395"),
( "junction between fundus and body on greater curvature", "None"),
# ( "lesser curvature of stomach", "UBERON:0001163", "FMA: 14572", "ILX:0733753"),
( "limiting ridge on greater curvature", "None"),
( "mucosa of stomach", "UBERON:0001199", "FMA:14907", "ILX:0736669"),
( "pylorus", "UBERON:0001166", " FMA:14581", "ILX:0734150"),
( "pyloric antrum", "UBERON:0001165", " FMA:14579", "ILX:0728672"),
( "pylorus on greater curvature", "None"),
( "pylorus on serosa split margin", "None"),
( "serosa of dorsal stomach", "None"),
( "serosa of stomach", "UBERON:0001201", "FMA:14914", "ILX:0735818"),
( "serosa split margin", "None"),
( "serosa of ventral stomach", "None"),
( "stomach", "UBERON:0000945", "FMA:7148", "ILX:0736697"),
( "ventral stomach", "None"),
("body of stomach", "UBERON:0001161", " FMA:14560", "ILX:0724929"),
("body-antrum junction along the greater curvature on circular-longitudinal muscle interface", "ILX:0793127"),
("body-antrum junction along the greater curvature on luminal surface", "ILX:0793128"),
("body-antrum junction along the greater curvature on serosa", "ILX:0793087"),
("cardia of stomach", "UBERON:0001162", " FMA:14561", "ILX:0729096"),
("circular muscle layer of stomach", "ILX:0774731"),
("circular-longitudinal muscle interface of body of stomach along the gastric-omentum attachment", "ILX:0793088"),
("circular-longitudinal muscle interface of dorsal stomach", "ILX:0793089"),
("circular-longitudinal muscle interface of duodenum along the gastric-omentum attachment", "ILX:0793090"),
("circular-longitudinal muscle interface of esophagus along the cut margin", "ILX:0793091"),
("circular-longitudinal muscle interface of fundus of stomach along the gastric-omentum attachment", "ILX:0793092"),
("circular-longitudinal muscle interface of gastroduodenal junction", "ILX:0793093"),
("circular-longitudinal muscle interface of pyloric antrum along the gastric-omentum attachment", "ILX:0793094"),
("circular-longitudinal muscle interface of pyloric canal along the gastric-omentum attachment", "ILX:0793095"),
("circular-longitudinal muscle interface of stomach", "ILX:0793096"),
("circular-longitudinal muscle interface of ventral stomach", "ILX:0793097"),
("dorsal stomach", "ILX:0793086"),
("duodenum", "UBERON:0002114", " FMA:7206", "ILX:0726125"),
("esophagogastric junction", "UBERON:0007650", "FMA: 9434", "ILX:0733910"),
("esophagogastric junction along the greater curvature on circular-longitudinal muscle interface", "ILX:0793098"),
("esophagogastric junction along the greater curvature on luminal surface", "ILX:0793099"),
("esophagogastric junction along the greater curvature on serosa", "ILX:0793100"),
("esophagogastric junction along the lesser curvature on circular-longitudinal muscle interface", "ILX:0793101"),
("esophagogastric junction along the lesser curvature on luminal surface", "ILX:0793102"),
("esophagogastric junction along the lesser curvature on serosa", "ILX:0793103"),
("esophagus", "UBERON:0001043", "FMA:7131", "ILX:0735017"),
("esophagus mucosa", "UBERON:0002469", "FMA:62996", "ILX:0725079"),
("esophagus smooth muscle circular layer", "UBERON:0009960", "FMA:67605", "ILX:0735992"),
("esophagus smooth muscle longitudinal layer", "UBERON:0009961", "FMA:63573", "ILX:0727608"),
("forestomach-glandular stomach junction", "UBERON:0012270", "ILX:0729974"),
("fundus of stomach", "UBERON:0001160", " FMA:14559", "ILX:0724443"),
("fundus-body junction along the greater curvature on circular-longitudinal muscle interface", "ILX:0793104"),
("fundus-body junction along the greater curvature on luminal surface", "ILX:0793105"),
("fundus-body junction along the greater curvature on serosa", "ILX:0793106"),
("gastroduodenal junction", "UBERON:0012650", "FMA:17046", "ILX:0725406"),
("gastroduodenal junction along the greater curvature on circular-longitudinal muscle interface", "ILX:0793107"),
("gastroduodenal junction along the greater curvature on luminal surface", "ILX:0793108"),
("gastroduodenal junction along the greater curvature on serosa", "ILX:0793109"),
("gastroduodenal junction along the lesser curvature on circular-longitudinal muscle interface", "ILX:0793110"),
("gastroduodenal junction along the lesser curvature on luminal surface", "ILX:0793111"),
("gastroduodenal junction along the lesser curvature on serosa", "ILX:0793112"),
("limiting ridge along the greater curvature on circular-longitudinal muscle interface", "ILX:0793113"),
("limiting ridge along the greater curvature on luminal surface", "ILX:0793114"),
("limiting ridge along the greater curvature on serosa", "ILX:0793115"),
("limiting ridge on circular-longitudinal muscle interface", "ILX:0793116"),
("limiting ridge on luminal surface", "ILX:0793117"),
("limiting ridge on serosa", "ILX:0793118"),
("longitudinal muscle layer of stomach", "ILX:0772619"),
("luminal surface of body of stomach", "ILX:0793119"),
("luminal surface of cardia of stomach", "ILX:0793120"),
("luminal surface of duodenum", "ILX:0793121"),
("luminal surface of esophagus", "ILX:0793122"),
("luminal surface of fundus of stomach", "ILX:0793123"),
("luminal surface of pyloric antrum", "ILX:0793124"),
("luminal surface of pyloric canal", "ILX:0793125"),
("luminal surface of stomach", "ILX:0793126"),
("mucosa of stomach", "UBERON:0001199", "FMA:14907", "ILX:0736669"),
("pyloric antrum", "UBERON:0001165", " FMA:14579", "ILX:0728672"),
("pyloric canal", "UBERON:0008858", "FMA:14580", "ILX:0735898"),
("serosa of body of stomach", "ILX:0771402"),
("serosa of cardia of stomach", "ILX:0776646"),
("serosa of duodenum", "UBERON:0003336", "FMA:14948", "ILX:0732373"),
("serosa of esophagus", "UBERON:0001975", "FMA:63057", "ILX:0725745"),
("serosa of fundus of stomach", "UBERON:0012503", "FMA:17073", "ILX:0726906"),
("serosa of pyloric antrum", "ILX:0777005"),
("serosa of pyloric canal", "ILX:0775898"),
("serosa of stomach", "UBERON:0001201", "FMA:14914", "ILX:0735818"),
("stomach", "UBERON:0000945", "FMA:7148", "ILX:0736697"),
("submucosa of esophagus", "UBERON:0001972", "FMA:62997", "ILX:0728662"),
("submucosa of stomach", "UBERON:0001200", "FMA:14908", "ILX:0732950"),
("ventral stomach", "ILX:0793085"),
]

def get_stomach_term(name : str):

def get_stomach_term(name: str):
"""
Find term by matching name to any identifier held for a term.
Raise exception if name not found.
:return ( preferred name, preferred id )
"""
for term in stomach_terms:
if name in term:
return ( term[0], term[1] )
return (term[0], term[1])
raise NameError("Stomach annotation term '" + name + "' not found.")
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